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4
votes
1answer
218 views

How the genome assembly be done after k-mer counting?

As far I know, before assembly of a genome, all k-mers from read should be counted. But after that, how the genome assembly be done? Is there any other thing needed along with k-mer counts? How ...
1
vote
1answer
35 views

How is output of DNA assembler measured?

I developed own DNA assembly pipeline. Input is set of reads and output is set of contigs. Many papers measure own algorithms and compare it against each other. There are basic metrics like: N50, ...
2
votes
3answers
213 views

What is the difference between sequence alignment and sequence assembly?

I read the wikipedia page about sequence alignment and sequence assembly but I have not been able to find any difference between the two. What is the difference between sequence alignment and sequence ...
0
votes
1answer
41 views

velvet assembler contig lengths are wrong [closed]

Has anyone else found that the contig length listed on the sequence defline, and in other files, is 32 nt shorter than the actual sequence? Any idea why this might be and what to do about it?
0
votes
1answer
88 views

What does the “cov” mean in a velvet assembler generated contig name?

A exmaple of a contig name generated by velvet assembler: NODE_127_length_39203_cov_244.873016 What does cov_244.873016 mean? ...
1
vote
1answer
142 views

How Scientists sequence, assemble and annotate plant genomes? [closed]

I previously read this question and this paper and learned good things about this topic. my current question is that scientists use which tools, algorithms, soft wares... to sequence, assemble and ...
4
votes
0answers
53 views

Which sequence assemblers I can use to compare different paradigms?

I'm a high school student whose interested in bioinformatics. Therefore I chose a project which I study Sequence Assembly. My main goal is to compare different paradigms (Greedy, OLC, De Bruijn). I ...
3
votes
0answers
31 views

Gibson assembly - primer design with A and T rich regions

I have question about Gibson assembly. I have done it several times and it always worked okay for us, but now I want to assemble together a fragment which has sequence like this: 5'...
2
votes
0answers
41 views

Assembly reconciliation

We have some bacterial genomes that were assembled using Spades, they were sequenced with and IonTorrent PGM. There are many assemblers and they give different results. I was interested in a tool ...
4
votes
2answers
807 views

Why is assembling paired end illumina without any input parameters an important problem?

In one of the comments in this question about multiple sequence alignment, it was stated @5heikki: btw if you want a good bioinformatics problem, come up with an assembler that assembles any ...
1
vote
0answers
268 views

Is the default kmer 25 value in Trinity still ok for assembly of 150bp reads from Illumina HiSeq 2500?

I will soon be receiving Illumina HiSeq 2500 data (150bp PE stranded reads). In the past we have been using Trinity as our assembler of choice, but it uses a default kmer value of 25. I believe this ...
5
votes
3answers
229 views

How easy is it to carry out de novo sequence assembly?

Today a colleague of mine asked the following question: " Assuming I need to build from 0, a chromosome of a fish, with short reads but no other reference whatsoever [de novo assembly]: ...
41
votes
4answers
3k views

What exactly are computers used for in DNA sequencing?

I've thoroughly read the Wikipedia article on DNA sequencing and can't get one thing. There's some hardcore chemistry involved in the process that somehow splits the DNA and then isolates its parts. ...